Update *07 Oct 2016*: New google policy does not allow swapping of primary domain with secondary domain anymore. But i found a tedious way which will be able to change your primary domain with your secondary domain, but your old primary domain will be deleted. Since the process is much more tedious, i will have to do it for $10 instead of $5. If you want to re-add the old primary domain as secondary domain, please use the extra gig, thanks.
I will help you change your primary domain or add secondary domain for your Google Apps (GApps) Free Standard account. Each account are only allowed maximum of 2 secondary domains
This gig about:-
change primary domain 'or' add one secondary domain
You can be assured of:
fast, reliable and customer happiness.